Use of a fluidic device

ABSTRACT

A fluidic device has a culture chamber configured to house a 3D culture matrix comprising a culture of microorganisms. A concentration gradient of a test substance is established over the 3D culture matrix by providing respective fluid flows at different end portions of the culture chamber and comprising different concentrations of the test substance. The response of the microorganisms to the test substance is determined based on the position of a border zone in the 3D culture matrix.

TECHNICAL FIELD

The embodiments generally relate to fluidic devices and in particular tothe use of such fluidic devices in determining a response ofmicroorganisms to test substances.

BACKGROUND

Antibiotic-resistant bacteria represent a growing global problem, asthese bacteria cannot be killed or made to stop dividing by antibiotics.The generation time of bacteria can in many cases be very fast (around20 minutes), and due to the short generation time and relative geneticinstability of bacteria, the bacteria may quickly acquire resistancetowards antibiotics. There is an increasing prevalence ofantibiotic-resistant bacterial infections in the human population, andsome of these bacteria have even become multi-resistant, sometimesmeaning that there are no efficient antibiotics available to halt theirgrowth. These multi-resistant bacteria are a serious public healthproblem as patients infected with such bacteria may die due to thattheir bacterial infections cannot be treated.

The traditional approaches for the identification and study ofmicroorganisms, including but not limited to bacteria, fungi, parasitesand viruses, and their resistance to antibiotics that kill or inhibitthe growth of the microorganism, have mainly in the example of bacteriabeen limited to Luria broth (LB) agar plates. These LB agar plates havethen been made to contain bactericidal and bacteriostatic antibiotics ofdefined concentrations. Such two-dimensional (2D) culture methods forantibiotic susceptibility testing (AST) and evaluation of the effects ofantibiotics or other test substances on microorganisms have severallimitations. For instance, these setups normally require that themicroorganisms, e.g. bacteria, are cultured over night to allow for aclear result readout showing if a particular bacteria strain isresistant or not to a given antibiotic. In addition, generally only asingle antibiotic concentration can be tested per LB agar plate.

Another prior art AST approach uses a so-called E-test. The E-test isbasically an agar diffusion method and uses a rectangular stripimpregnated with different concentrations of a test substance to beevaluated for its effect as an antibiotic. In a typical approach,bacteria are spread and grown in a 2D culture on top of an agar plate,where after the E-test strip is placed on top of the agar plate. TheE-test strip releases the test substance by diffusion and the growthinhibitory effects of the released test substance are typicallyinspected after 24 hours of incubation. A limitation of this approachis, in addition to the very long incubation time, that readouts of theinhibitory concentration of the test substance is only possible indistinct digital steps and in the selected concentrations used in theE-test strip.

A further traditional AST approach uses a microtiter plate assay withdifferent concentrations of a test substance in different wells. Themicrotiter plate with added bacteria is usually incubated overnight andthe inhibitory effects on the bacteria are evaluated by measuring theoptical turbidity in the different wells. This approach has basicallythe same shortcomings as when using E-test strips.

In order to reduce the AST time, microfluidic channel systems for rapidAST (RAST) have been developed. Such RAST approaches includedroplet-based microfluidic channel systems in which bacteria arecaptured in a droplet that includes an antibiotic [1-3]. A limitationwith the droplet-based system is that only a single antibioticconcentration can be tested. Other RAST approaches include using gaspermeable polydimethylsiloxane (PDMS) microchannels [4],dielectrophoretic capturing of bacteria in microfluidic electrodestructures [5-6], preloaded PDMS layers with antibiotics [7], covalentlybinding bacteria to microfluidic channels and subjecting them tomechanical shear stress [8], using asynchronous magnetic bead rotation(AMBR) biosensors [9] or tracking single cell growth in a microfluidicagarose channel system [10]. A major limitation of these various RASTapproaches is that they can only test a single antibiotic concentrationor a set of a few selected antibiotic concentrations.

It has further been proposed to use a microfluidic system for analysisof antibiotic susceptibility of bacterial biofilms [11]. Theirmicrofluidic system, however, requires 24 hours of incubation and thatthe bacteria to be tested contain a plasmid able to express greenfluorescent protein (GFP).

Hence, there is still a need for fast methods and systems for responsetesting of microorganism that do not have the disadvantages of the priorart.

SUMMARY

It is a general objective to enable efficient and fast determination ofthe response of microorganisms to test substances.

This and other objectives are met by embodiments as defined herein.

An aspect of the embodiments relates to a method of determining aresponse of a microorganism to a test substance. The method comprisesproviding a culture of the microorganism in a three-dimensional (3D)culture matrix arranged in a culture chamber of a fluidic device havinga first fluid channel flanking a first end portion of the culturechamber and a second fluid channel flanking a second, different endportion of the culture chamber. The method also comprises connecting aninput of the first fluid channel to a first fluid flow comprising thetest substance at a first concentration. The method further comprisesconnecting an input of the second fluid channel to a second fluid flowlacking the test substance or comprising the test substance at a secondconcentration that is lower than the first concentration to from aconcentration gradient of the test substance over at least a portion ofthe 3D culture matrix. The method additionally comprises determining aresponse of the microorganism to the test substance based on a positionof any border zone in the 3D culture matrix relative to the first endportion and/or the second, different end portion. The border zone isbetween a first response zone in which the microorganism shows a firstresponse to the test substance and a second response zone in which themicroorganism shows a second, different response to the test substance.

Another aspect of the embodiments relates to a system for determining aresponse of a microorganism to a test substance. The system comprises afluidic device comprising a culture chamber configured to house aculture of the microorganism in a 3D culture matrix. The fluidic devicealso comprises a first fluid channel flanking a first end portion of theculture chamber and a second fluid channel flanking a second, differentend portion of the culture chamber. The system also comprises a firstfluid reservoir comprising a first fluid comprising the test substanceat a first concentration. The first fluid reservoir is configured to beconnected to an input of the first fluid channel. The system furthercomprises a second fluid reservoir comprising a second fluid lacking thetest substance or comprising the test substance at a secondconcentration that is lower than the first concentration. The secondfluid reservoir is configured to be connected to an input of the secondfluid channel to form a concentration gradient of the test substanceover at least a portion of the 3D culture matrix. The systemadditionally comprises a computer-based system configured to take atleast one image of the 3D culture matrix and process the at least oneimage to identify a position, relative to the first end portion and/orsecond end, different portion, of any border zone in the 3D culturematrix. The border zone is between a first response zone in which themicroorganism shows a first response to the test substance and a secondresponse zone in which the microorganism shows a second, differentresponse to the test substance. The computer-based system is alsoconfigured to determine a response of the microorganism to the testsubstance based on the position of the border zone.

A further aspect of the embodiments relates to use of a fluidic deviceto determine a response of a microorganism to a test substance. Thefluidic device comprises a culture chamber configured to house a cultureof the microorganism in a 3D culture matrix. The fluidic device alsocomprises a first fluid channel flanking a first end portion of theculture chamber and configured to carry a first fluid flow comprisingthe test substance at a first concentration. The fluidic device furthercomprises a second fluid channel flanking a second, different endportion of the culture chamber and configured to carry a second fluidlacking the test substance or comprising the test substance at a secondconcentration that is lower than the first concentration to form aconcentration gradient of the test substance over at least a portion ofthe 3D culture matrix. The use comprises determining the response of themicroorganism to the test substance based on a position of any borderzone in the 3D culture matrix relative to the first end portion and/orthe second, different end portion. The border zone is between a firstresponse zone in which the microorganism shows a first response to thetest substance and a second response zone in which the microorganismshows a second, different response to the test substance.

The aspects of the embodiments enable a very quick and efficientdetermination of the response of microorganisms to various testsubstances. The response of microorganisms to a continuous range ofconcentrations can be tested according to the embodiments.

BRIEF DESCRIPTION OF THE DRAWINGS

The embodiments, together with further objects and advantages thereof,may best be understood by making reference to the following descriptiontaken together with the accompanying drawings, in which:

FIG. 1 is a flow diagram illustrating a method of determining a responseof a microorganism to a test substance according to an embodiment;

FIG. 2 is a flow diagram illustrating an embodiment of the connectingsteps in FIG. 1;

FIG. 3 is a flow diagram illustrating additional, optional steps of themethod in FIG. 1 according to an embodiment;

FIG. 4 is a flow diagram illustrating an additional, optional step ofthe method in FIG. 1 according to an embodiment;

FIG. 5 is a flow diagram illustrating an additional, optional step ofthe method in FIG. 1 according to an embodiment;

FIG. 6 is a flow diagram illustrating additional, optional steps of themethod in FIG. 3 according to an embodiment;

FIG. 7 is a flow diagram illustrating an embodiment of the determiningMIC step in FIG. 6;

FIG. 8 is a schematic overview of a microfluidic device and a 3D culturematrix with microorganisms according to an embodiment;

FIG. 9 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to an embodiment;

FIG. 10 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to another embodiment;

FIG. 11 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to a further embodiment;

FIG. 12 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to yet another embodiment;

FIG. 13 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to a further embodiment;

FIG. 14 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to still another embodiment;

FIG. 15 is a schematic illustration of a culture chamber and fluidchannels of a microfluidic device according to yet another embodiment;

FIG. 16 schematically illustrates a system for determining a response ofa microorganism to a test substance according to an embodiment togetherwith a time series showing formation of a concentration gradient in the3D culture matrix;

FIG. 17A illustrates an image taken of a 3D culture matrix followingformation of a linear gradient of ampicillin (20-0 μg/ml left to right)through the 3D culture matrix with E. coli K12 MG1655 (the black boxindicates the selected area for intensity measurements);

FIG. 17B illustrates an intensity profile of the selected area in FIG.17A with an intensity increase at 5 μg/ml indicating the minimuminhibitory concentration of E. coli K12 MG1655 for ampicillin;

FIG. 17C schematically illustrates the linear gradient of ampicillin(20-0 μg/ml) through the 3D culture matrix of FIG. 17A;

FIG. 18A illustrates an image taken of a 3D culture matrix followingformation of a linear gradient of spectinomycin (50-0 μg/ml left toright) through the 3D matrix with E. coli K12 MG1655 (the black boxindicates the selected area for intensity measurements);

FIG. 18B illustrates an intensity profile of the selected area in FIG.18A;

FIG. 18C schematically illustrates the linear gradient of spectinomycin(50-0 μg/ml) through the 3D culture matrix of FIG. 18A;

FIG. 19 is a diagram showing growth curves over time for E. coli K12MG1655 exposed to various concentrations of spectinomycin; and

FIG. 20 schematically illustrates the results of culturing cells in amicrofluidic device with a stable and continues gradient of anantimicrobial.

DETAILED DESCRIPTION

Throughout the drawings, the same reference numbers are used for similaror corresponding elements.

The present embodiments generally relate to fluidic devices and inparticular to the use of such fluidic devices in determining responsesof microorganisms to test substances. It has been concluded that fluidicdevices, such as microfluidic devices, can be designed to beparticularly suitable to monitor or determine the response ofmicroorganisms to various test substances. In more detail, such fluidicdevices, having a culture chamber with a three-dimensional (3D) culturematrix containing a culture of the relevant microorganisms, provide anefficient tool to quickly determine the response of the microorganismsto the test substance or indeed to any combination of multiple testsubstances.

Such fluidic devices have key features that make them a very efficienttool. Firstly, a steady-state gradient of the relevant test substancecan quickly and accurately be established over at least a portion of the3D culture matrix. This means that a continuous range of test substanceconcentrations is established from a high concentration at one of theend portions or sides of the 3D culture matrix down to a low or zeroconcentration at another end portion or side of the 3D culture matrix.Hence, a continuous range of concentrations of the test substance can betested with a single fluidic device. This is in clear contrast to priorart techniques where one or at most a few predefined concentrations butnot any continuous range of concentrations can be tested. Accordingly, amore exact determination of, for instance, minimum inhibitoryconcentration of an antibiotic can be made.

Secondly, the microorganisms are cultured in a 3D culture matrix.Accordingly, the microorganisms are allowed to grow in three dimensions.This in turn provides a much more significant difference between areasof the 3D culture matrix where viable and growing microorganisms arepresent and areas with cell death or low growth. Accordingly, theembodiments provide an enhanced signal-to-noise ratio. Hence, it is mucheasier to differentiate between different areas or zones in the 3Dculture matrix as compared to growing microorganisms as a biofilm on atwo-dimensional (2D) surface where fewer microorganisms can be grownand, thus, lower detection signals are generated.

A gradient of the test substance can quickly be established over atleast a portion of the 3D culture matrix. This together with thepossibility of microorganism growth in three dimensions enables readingthe response of the microorganisms to the test substance in a very shorttime, generally within one or at most a few hours. This should becompared to several of the prior art techniques, typically requiringincubation overnight.

The fluidic device is advantageously provided as a small-scale device,i.e. a microfluidic device or even a nanofluidic device. Accordingly,small amounts of the test substance and the microorganisms are needed tosuccessfully run a test.

Determining or monitoring the response of the microorganisms to the testsubstance can be made using common microscopy or indeed even by thehuman eye. Hence, generally no complex and specifically designeddetection equipment is needed in order to determine the response of themicroorganisms to the test substance.

The embodiments use a fluidic device in the monitoring and determinationof the response of microorganisms to various test substances. A fluidicdevice, also referred herein as a fluidic culture device, implies thatfluid flows are present in channels of the fluidic device in order totransport the test substance to a culture chamber and thereby furtherinto the 3D culture matrix present in the culture chamber.

The fluidic device is advantageously a so-called microfluidic device ormicrofluidic culture device. Microfluidic implies that the fluidchannels of the microfluidic device are microsized channels. Generally,for such fluid channels with dimensions in the sub-micrometer range, theexpression nanofluidics is often used. Hence, the fluidic device of theembodiments could also be such a nanofluidic device or nanofluidicculture device.

The fluid channels of the fluidic culture device are configured to carrya respective fluid flow. The fluid flow is preferably a liquid flow of aliquid in the fluid channel. However, it is also possible to have a flowof gas in the fluid channel or indeed a flow of fluidized solids orparticles. Also a liquid flow with dissolved gas therein can be usedaccording to the embodiments.

In a general embodiment, the fluidic device 1, see FIG. 8, comprises aculture chamber 10 configured to house a culture of a microorganism 6 ina 3D culture matrix 2. The fluidic device 1 also comprises a first fluidchannel 20 flanking a first end portion or side 12 of the culturechamber 10 and a second fluid channel flanking a second, different endportion or side 14 of the culture chamber 10. The first fluid channel 20is then configured to carry a first fluid flow comprising a testsubstance at a first concentration. The second fluid channel 30 iscorrespondingly configured to carry a second fluid flow lacking the testsubstance or comprising the test substance at a second concentrationthat is lower than the first concentration to form a concentrationgradient of the test substance over at least a portion of the 3D culturematrix 2.

In order to form a concentration gradient of the test substance over atleast a portion of the 3D culture matrix 2 the two fluid flows shouldcomprise the test substance at different concentrations. Herein, thefirst fluid flow is defined as the fluid flow that comprises the testsubstance at the highest concentration. This means that the second fluidflow either lacks the test substance or comprises the test substance ata different, i.e. lower, concentration as compared to the first fluidflow.

The two fluid flows preferably have the same ingredient(s) orconstituent(s) with the exception of one or more test substances to betested. Hence, if the fluid flows are liquid flows the first and secondfluid flows preferably comprise the same liquid or liquid mixture towhich the test substance is added at the selected first concentration orthe selected first and second concentrations. Correspondingly, if thetwo fluid flows are gas flows the first and second fluid flowspreferably comprise the same gas or gas mixture to which the testsubstance is added at the selected concentration(s).

The embodiments can generally use any fluidic device having a culturechamber configured to house a 3D culture matrix and being flanked atdifferent end portions with respective fluid channels. There are severalsuch fluidic channels available in the art. For instance, a microfluidicdevice that works excellent according to the embodiments is marketed asCELLDIRECTOR® Ruby by Gradientech AB (Uppsala, Sweden). Fluidic devicesthat can be used according to the embodiments are also disclosed in, forinstance, the following references [12-17, 19], the teachings of whichwith regard to microfluidic devices are hereby incorporated byreference.

FIG. 20 schematically illustrates injecting a gel and cell mixture intoa culture chamber of a microfluidic device. The cells are initiallyevenly distributed in the formed 3D culture matrix. In the illustrativeexample, a stable and continuous gradient was established by providing afirst fluid flow comprising an antimicrobial and a second fluid flowlacking the antimicrobial. The gradient is thereby established over theculture chamber and the 3D culture matrix. The lower figure illustratesthe result of culturing the cells in the 3D culture matrix and exposingthem to the gradient of the antimicrobial.

FIG. 1 is a flow diagram of a method of determining a response of amicroorganism to a test substance according to an embodiment. The methodcomprises providing, in step S1, a culture of the microorganism in a 3Dculture matrix arranged in a culture chamber of a fluidic device. Thisfluidic device has a first fluid channel flanking a first end portion orside of the culture chamber and a second fluid channel flanking asecond, different end portion or side of the culture chamber. A nextstep S2 comprises connecting an input of the first fluid channel to afirst fluid flow comprising the test substance at a first concentration.Step S3 correspondingly comprises connecting an input of the secondfluid channel to a second fluid flow lacking the test substance orcomprising the test substance at a second concentration that is lowerthan the first concentration. Consequently, a concentration gradient ofthe test substance is thereby formed over at least a portion of the 3Dculture matrix. A next step S4 determines a response of themicroorganism to the test substance based on a position of any borderzone in the 3D culture matrix relative to the first end portion or sideand/or relative to the second, different end portion or side. Thisborder zone is present between a first response zone in which themicroorganism shows a first response to the test substance and a secondresponse zone in which the microorganism shows a second, differentresponse to the test substance.

The two steps S2 and S3 can be performed serially in any order, i.e.step S2 prior to or after step S3. Alternatively, the two steps S2 andS3 are performed at least partly in parallel.

The responses of the microorganisms in the 3D culture matrix to the testsubstance imply that at least three clearly visible zones will generallybe present. These zones include the first response zone in which themicroorganisms show a first response to the test substance. This firstresponse zone is the zone closest to the first end portion or side andthe first fluid channel. Hence, the first response zone corresponds tothe portion of the 3D culture matrix exposed to a higher concentrationof the test substance. The zones also include the second response zonein which the microorganisms show a second response to the test substanceand where this second response is different from the first response. Thesecond response zone is the zone closest to the second end portion orside and the second fluid channel. Hence, the second response zonecorresponds to the portion of the 3D culture matrix exposed to a lowerconcentration of the test substance.

The border zone then constitutes the portion of the 3D culture matrixpresent in between the first response zone and the second response zone.This border zone 5 could be very thin, basically a boundary or borderbetween the first response zone 3 and the second response zone 4 asshown in FIG. 17A. Alternatively, the border zone 5 has a widerextension in the 3D culture matrix between the first and second endportions or sides as shown in FIG. 18A.

The border zone thereby constitutes the portion of the 3D culture matrixwhere the local concentration of the test substance achieves a shift orchange in response to the test substance from the first response in thefirst response zone to the second response in the second response zone.

For instance, if the test substance is an antibiotic or anotherbactericide or bacteriostat the second response zone, in which themicroorganisms, here represented by bacteria, are exposed to acomparatively low concentration of the test substance, could be theportion of the 3D culture matrix with viable and growing bacteria. Thefirst response zone is then preferably the portion of the 3D culturematrix where there is substantially no viable or growing bacteria, hencethe first response zone is characterized by a relative lack of bacteria(due to cell death or no cell growth). The border zone then constitutesthe border or portion between the growing/viable portion and thenon-growing/cell death portion.

FIG. 17A clearly shows a second response zone 4 with growing bacteria(seen as white signal in the figure). In this portion of the 3D culturematrix the concentration of the test substance, here ampicillin, is toolow to prevent cell growth or induce cell death among the Escherichiacoli K12 MG1655 bacteria. In the first response zone 3 the concentrationof ampicillin is, however, sufficiently high to prevent cell growth orinduce cell death. Hence, substantially no E. coli K12 MG1655 are seenin this portion of the 3D culture matrix. In the shown experiment theborder zone 5 is basically a clear border or boundary defining theminimum inhibitory concentration (MIC) of ampicillin for this particularE. coli strain.

In FIG. 18A the situation is somewhat different with a broader borderzone 5 in between the second response zone 4 with viable and growing E.coli K12 MG1655 and the first response zone 3 where the concentration ofspectinomycin as test substance was sufficiently high to kill thebacteria or at least prevent growth of any bacteria. In this experiment,some of the E. coli K12 MG1655 show resistance to the antibioticspectinomycin as shown by some viable and growing bacteria in the borderzone 5. The amount of bacteria in this border zone 5 is, however,significantly lower and different from the amount of bacteria in thesecond response zone 4 as clearly shown in FIG. 18A.

In a corresponding setting where the motility response of microorganismsis to be tested the second response zone could be the portion of the 3Dculture matrix with low or no motility of the microorganisms (if thetest substance induced motility among otherwise rather immobilemicroorganisms) or with high motility of the microorganisms (if themicroorganisms are motile and the test substance inhibits thismotility). The first response zone could then be the portion of the 3Dculture matrix with sufficiently high concentration of the testsubstance to induce motility among the microorganisms or inhibitmotility of the microorganisms. The border zone is then the portion ofthe 3D culture matrix between the first and second response zones and ischaracterized by the switch or change in motility from the immobile/lowmotility portion on one side of the border zone to the motile/highmotility portion on the other side of the border zone. The border zonecould then be a clear border or boundary similar to FIG. 17A or a widerportion with some intermediate motility of the microorganisms.

Motility and cell death are merely examples of responses ofmicroorganisms that can be monitored and determined according to theembodiments. Other, non-limiting, examples include cell growth,proliferation, response behaviour to various forms of induced stress,matrix adhesion, mutability, etc.

The microorganisms, the response of which is to be determined, can beany microorganisms that can be grown and cultured in a 3D culture matrixof the fluidic device. Non-limiting examples of such microorganismsinclude bacteria, fungi, parasites, viruses and also cells, such ashuman cells or other mammalian cells. A single species or strain of themicroorganisms could be tested and thereby cultured in the 3D culturematrix. Alternatively, a combined response of multiple, i.e. at leasttwo, microorganisms could be determined. In such an approach, multipledifferent microorganisms are co-cultured in the 3D culture matrix.

The 3D culture matrix can be made of any material that is suitable as aculture matrix for the relevant microorganism(s). Such a material can beselected among traditionally used materials for cell cultures. Preferredbut non-limiting examples of materials include agar; agarose; collagenI; extracellular matrix (ECM) gels, such as MATRIGEL™; hydrogels, suchas a mixture of phenylalanine (Phe) dipeptide formed by solid-phasesynthesis with a fluorenylmethoxycarbonyl (Fmoc) protector group on theN-terminus, and Fmoc-protected lysine (Lys) or solely phenylalanine.

In a particular embodiment, the microorganisms are of one bacteriumstrain and the test substance is an antibiotic and the MIC of theantibiotic is determined by the fluidic device.

The response of the microorganisms in the 3D culture matrix to the testsubstance is determined in step S4 of FIG. 1 based on the position ofthe border zone relative to the first and/or second end portion or sideof the culture chamber. This position of the border zone relative to theend portions or sides of the culture chamber correlates to aconcentration or at least a concentration range of the test substance.Hence, the position of the border zone or the distance between theborder zone and the first end portion or side and/or the distancebetween the border zone and the second, different end portion or sidecorresponds to a concentration or concentration range of the testsubstance. Accordingly, it is possible to accurately determine theconcentration or concentration range at which the response of themicroorganisms changes or switches from the first response in the firstresponse zone to the second response in the second response zone.

This further means that the position of the border zone can thereby betransformed or converted into, for instance, a MIC of an antibiotic, amotility inhibitory/promoting concentration of a test substance thatinhibits/induces motility of the microorganisms, an adhesioninhibitory/promoting concentration of a test substance thatinhibits/induces matrix adhesion of the microorganisms, etc.

In a particular embodiment, step S4 comprises determining the responseof the microorganism to the test substance based on the position,relative to the first end portion and/or second, different end portion,of the border zone in the 3D culture matrix and based on the width ofthe border zone. Hence, in this particular embodiment, not only theposition of the border zone, i.e. the distance between border zone andthe first and/or second end portion of the culture chamber, but also thewidth of the border zone is used when determining the response. Forinstance, if the width of the border zone is substantially zero (seeFIG. 17A), i.e. basically a boundary or border between the first andsecond response zones, the change in response of the microorganismsoccurs at a specific concentration of the test substance. However, ifthe border zone has a non-zero width (see FIG. 18A) the change inresponse of the microorganisms occurs at a concentration rangecorresponding to the respective ends of the border zone.

A border zone with a non-zero width may further provide information withregard to any resistance of the microorganisms to the test substance.Hence, an extended border zone may imply that a resistance to the testsubstance is present in some of the microorganisms, for instance sincethey are able to grow at concentrations of the test substance whichotherwise kill or prevent growth to non-resistant microorganisms. Thismeans that the width of the border zone can be used in order todetermine or detect any resistance at a given time of the microorganismsto the test substance.

In fact, it is actually possible with the fluidic device and method ofthe embodiments to detect any mutation in the microorganisms thatinduced resistance to the test substance or indeed caused loss ofresistance to the test substance. Thus, the width of the border zoneover time could be monitored when running the fluidic device with theculture of microorganisms in the 3D culture matrix and with the firstand second fluid flows through the first and second fluid channels. Anincrease in the width of the border zone over time then typicallyimplies gain of resistance to the test substance among at least some ofthe microorganisms. Correspondingly, a decrease in the width of theborder zone typically implies loss of resistance to the test substanceamong microorganisms that previously showed resistance to the testsubstance.

Accordingly, in a particular embodiment it is preferred to use not onlythe position of the border zone but also its width when determining theresponse of the microorganisms to the test substance.

In more complex set-ups and arrangements of the fluidic device usingmultiple test substances and gradients, not only the width of the borderzone or border zones may be of relevance. In these cases, also, orinstead, the actual shape of the border zone(s) could be descriptive ofthe response of the microorganisms to the test substance(s). The shapeof the border zone(s) could then encompass parameters such as area,curvature, width in different directions, etc. Hence, in a particularembodiment, the position of the border zone and the shape of the borderzone are used when determining the response of the microorganisms to thetest substance(s).

FIG. 2 is a flow diagram illustrating steps S2 and S3 in FIG. 1according to a particular embodiment. This figure with be furtherdescribed below with further reference to FIG. 8 and the fluidic device1 shown therein. The method continues from step S1 in FIG. 1. A nextstep S10 comprises connecting the input 22 of the first fluid channel 20to a first fluid reservoir 26 comprising a first fluid with the testsubstance at the first concentration. A next step S11 comprises pumpingor otherwise providing the first fluid from the first fluid reservoir 26into the input 22 of the first fluid channel 20 and out through anoutput 24 of the first fluid channel 20.

Step S12 comprises connecting the input 32 of the second fluid channel30 to a second fluid reservoir 36 comprising a second fluid lacking thetest substance or comprising the test substance at the secondconcentration. The following step S13 comprises pumping or otherwiseproviding the second fluid from the second fluid reservoir 36 into theinput 32 of the second fluid channel 30 and out through an output 34 ofthe second fluid channel 30. The method then continues to step S4 ofFIG. 1.

Hence, in a particular embodiment each fluid channel 20, 30 is connectedto a fluid reservoir 26, 36 comprising the fluid to flow through thefluid channel 20, 30 and transport the test substance to the 3D culturematrix 2 in the culture chamber 10. The fluids can be drawn from thefluid reservoirs 26, 36 and into the fluid channels 20, 30 using anyequipment (not shown) capable of establishing a flow of the fluidsthrough the fluid channels 20, 30. Typically, fluid pumps or pushers arearranged in the fluid paths from the fluid reservoirs 26, 36 and theinputs 22, 32 of the fluid channels 20, 30 and/or connected to theoutput(s) 24, 34 of the fluid channels 20, 30. It may be possible use asingle pump or pusher that operates on both fluid paths.

In FIG. 8 the fluid channels 20, 30 have a common output 24, 34. Hence,the first fluid channel 20 and the second fluid channel 30 merge at apoint downstream of the culture chamber 10. In an alternative approach,each fluid channel 20, 30 has a respective output 24, 34.

The pumping of the fluids from the reservoirs 26, 36 into the inputs 22,32 of the fluid channels 20, 30 is preferably performed throughout theusage or operation of the fluidic device 1 to determine the response.Hence, the pumping of the fluid is preferably performed at least untilthe response of the microorganisms 6 to the test substance has beendetermined.

The fluids present in the two fluid reservoirs 26, 36 are preferably thesame fluid with the exception of the respective concentrations of thetest substance(s).

Providing an even and non-fluctuating flow of the fluids through thefluid channels 20, 30 implies that a gradient of the test substance willbe established over at least a portion of the 3D cell matrix 2. Thismeans that when the fluid channels 20, 30 are connected to the fluidreservoirs 26, 36 and pumping of the fluids through the channels hasjust started no concentration gradient of the test substance has yetestablished over the 3D culture matrix 10. In clear contrast, the firstend portion or side 12 of the culture chamber 10 is exposed to the firstconcentration of the test substance and the second end portion or side14 of the culture chamber 20 is exposed to the second concentration ofthe test substance or is not exposed to the test substance at all. Atthis point substantially no test substance has diffused into the 3Dculture matrix 2, which then typically has a zero concentration of thetest substance. Over time the test substance is diffusing from the firstfluid in the first fluid channel 20 into the 3D culture matrix 2.Eventually, a steady-state concentration gradient of the test substanceis established over at least a portion of the 3D culture matrix 2 withthe first end of the 3D culture matrix 2 facing the first fluid channel20 having the first concentration of the test substance and the secondend of the 3D culture matrix 2 facing the second fluid channel 20 havingzero or the second concentration of the test substance.

In FIG. 2 a fluidic device 1 with two fluid channels 20, 30 have beenassumed. If more than two fluid channels 20, 30 flank respective endportions of the culture chamber 10 then a respective connecting andpumping step is preferably performed for each such fluid channel.

In FIG. 2 the steps have been presented in a serial order. Steps S10 andS12 can be performed serially in any order or at least partly inparallel. The pumping of steps S11 and S13 are typically performed inparallel and throughout the whole usage or operation of the fluidicdevice 1.

Hence, in a particular embodiment the method comprises an additionalstep S30 as shown in FIG. 4. The method continues from step S3 of FIG. 1or indeed from step S13 in FIG. 2. This additional step S30 comprisesestablishing a concentration gradient over at least a portion of the 3Dculture matrix by diffusion of the test substance from the first fluidflow into the 3D culture matrix 2. This diffusion of the test substanceis preferably achieved with substantially no flow of the first or secondfluid through the 3D culture matrix.

Hence, the diffusion is from a so-called source fluid channel 20, whichhas a higher concentration of the test substance in the fluid relativethe other fluid channel, denoted sink fluid channel 30. In a preferredembodiment, the flow rates of the fluids in the two fluid channels 20,30 are preferably kept substantially similar since then no flow of thefluid is present through the 3D culture matrix 2 in the culture chamber10. Substantially similar indicates that the two flow rates arepreferably identical but can differ slightly due to inherent variationsin the flow rate of the pumping systems. Thus, the difference in flowrate in the two fluid channels 20, 30 are preferably less than 10%, morepreferably less than 5%, such as less than 2.5% and most preferably lessthan 1%.

If there is no net flow of the fluid over the 3D culture matrix 2 andthe parts of the fluid channels 20, 30 adjacent a culture chamber 10with a rectangular or quadratic bottom area, then the concentrationgradient over the 3D culture matrix 2 will be linear.

The concentration gradient of the test substance can be established overthe whole 3D culture matrix or over a portion of the 3D culture matrixdepending on the positions of the fluid channels relative to the culturechamber and the shape of the culture chamber and the 3D culture matrixarranged therein.

In an embodiment, the respective concentrations of the test substance inthe two fluid flows are fixed throughout the procedure. Hence, in such acase, the first concentration and the second concentration (if non-zero)are preferably fixed. In another embodiment, it is possible to change oradjust the concentration of the test substance in at least in one of thefluid flows during the procedure. Such a change could be in terms of oneor more steps in concentration, i.e. switching from an initialconcentration to a new concentration of the test substance.Alternatively, the change in concentration could be gradual and overtime.

A change in concentrations could, for instance, be used if the initialconcentrations of the test substance in the fluid flows did not resultin any detectable effect. For instance, a too low concentration of anantibiotic in both fluid flows and thereby obtaining microorganismgrowth throughout the whole 3D culture matrix could be a case where itis appropriate to increase the concentration of the antibiotic in atleast the first fluid channel.

A change in the concentration of the test substance in at least one ofthe fluid flows can also be used in various stress tests.

FIG. 3 is a flow diagram illustrating additional steps of the methodaccording to various embodiments. In an embodiment, the method continuesfrom step S3 of FIG. 1 (or from step S13 in FIG. 2 or step S30 in FIG.4). A next step S21, in this embodiment, comprises taking at least oneimage or picture of the 3D culture matrix. The border zone is thenidentified in the at least one image in step S22. The method thencontinues to step S4 of FIG. 1, where the response of the microorganismto the test substance is determined based on the position of the borderzone relative to the first and/or second end portion or side of the 3Dculture matrix and where this position is identified in the at least oneimage.

Hence, one or more images are taken of the 3D culture matrix and theborder zone is then identified in at least one of these images. Theposition of the border zone and optionally also the width and/or shapeof the border zone can then be determined, either manually from theimage, or by image processing using suitable equipment as is furtherdisclosed herein.

In a particular embodiment, the at least one image of the 3D culturematrix is taken in step S21 using a bright-field microscope or using aphase-contrast microscope. In such a case, the position and optionallythe width and/or shape of the border zone can be identified based on thedetected light intensity in the at least one image. In an embodiment,step S22 therefore comprises processing the at least one image by acomputer configured to identify the border zone based on detected lightintensity in the at least one image.

Hence, in most embodiments there will be a clear visual differencebetween the first response zone and the second response in an imagetaken using a bright-field or phase-contrast microscope of the 3Dculture matrix. As a consequence, the light intensity detected in theimage can be used to manually, or using a computer with suitableimage-processing program or software, identify the position andoptionally the width and/or shape of the border zone in the image. Thismeans that in most practical embodiments no staining or labelling of themicroorganisms is needed.

It is, however, possible to have an additional, optional step S20, whichcomprises adding at least one fluorescent label to the 3D culturematrix. This fluorescent label is then configured to bind to themicroorganism or to be taken up by the microorganism. In such a case,the at least one image of the 3D culture matrix is preferably takenusing a fluorescent or confocal microscope in step S21. The border zonecan then be identified in step S22 by processing the at least one imageby a computer configured to identify the border zone based on detectedfluorescence in the at least one image. Alternatively, manual inspectionof the at least one image could be used to identify the border zone(position and optional width and/or shape) based on the fluorescence inthe at least image.

In the above described embodiment, at least one fluorescent label hasbeen added to the 3D culture matrix. In an alternative approach, themicroorganisms could themselves express at least one substance, such asfluorescent substance, that could be detected in an image taken using afluorescence or confocal microscope, or indeed any other imagingtechnique. Alternatively, the microorganisms can be made to express sucha substance, for instance by transfection of an engineered expressionvector that encodes such a substance. Hence, in such approaches theaddition of the fluorescent label in step S20 could be omitted.

In a preferred embodiment, step S21 comprises taking at least one imageof the 3D culture matrix at least after formation of a steady-stateconcentration gradient of the test substance over at least a portion ofthe 3D culture matrix. Hence, in a particular approach it is preferredto first establish the steady-state concentration gradient beforedetermining the response of the microorganisms to the test substance.Thus, the at least one image to be taken and analyzed or processed inorder to identify the border zone is preferably taken after formation ofsuch a steady-state concentration gradient.

Also, prior to reaching steady-state, the formation of the gradient ispredictable and can in some cases be directly visualized using, forexample, a fluorescent compound, thus enabling a readout of amicroorganism response in relation to a known concentration of the testsubstance already prior to achieving a steady state gradient.

A single image could be taken of the 3D culture matrix in step S21.Alternatively, images of the 3D culture matrix are periodically takenwithin an interval of, for instance, 0 to 12 hours from connecting theinputs of the fluid channels to the respective fluid flows. In aparticular embodiment, the time interval during which images areperiodically taken is preferably 0 to 6 hours, or 0 to 4 hours, or 0 to3 hours, or more preferably 0 to 2 hours or 0 to 1 hour followingstarting the monitoring by connecting the fluid channels to therespective fluid flows.

In the foregoing, the discussion has mainly been towards determining theresponse to a single test substance in the fluid device. However, it isalso possible to simultaneously determine the response to multiple testsubstances, determining the response to a mixture of multiple testsubstances or indeed determining different responses to multiple testsubstances or mixtures thereof.

In an embodiment, step S2 of FIG. 1 thereby comprises connecting theinput of the first fluid channel to a first fluid flow comprising afirst test substance at the first concentration and lacking a secondtest substance or comprising the second test substance at a thirdconcentration. Step S3 then comprises connecting the input of the secondfluid channel to a second fluid flow lacking the first test substance orcomprising the first test substance at the second concentration (that islower than the first concentration) and comprising the second testsubstance at a fourth concentration that is higher than the thirdconcentration. A first concentration gradient of the first testsubstance and a second concentration gradient of the second testsubstance are thereby formed over at least a portion of the 3D culturematrix.

Step S4 comprises, in this embodiment, determining a response of themicroorganism to the first test substance and the second substance basedon respective positions of any border zones in the 3D culture matrixrelative to the first and/or second end portion or side of the culturechamber. The border zone is between a first response zone in which themicroorganism shows a first response to the first test substance and thesecond test substance and a respective second response zone in which themicroorganism shows a second, different response to the first testsubstance and the second test substance.

Hence, in this embodiment a concentration gradient of the first testsubstance is established from the first fluid channel (highconcentration of the first test substance) over at least a portion ofthe 3D culture matrix to the second fluid channel (low concentration ofthe first test substance). Correspondingly, a concentration gradient ofthe second test substance is established from the second fluid channel(high concentration of the second test substance) over at least aportion of the 3D culture matrix to the first fluid channel (lowconcentration of the second test substance).

If the test substances, for example, are different antibiotics it couldbe possible that two border zones are present. In one case, whentravelling from the first fluid channel towards the second fluid channelthe 3D culture matrix could be dived among the following zones: a first“death” zone with no viable or growing microorganisms, a first borderzone, a growth zone with viable and growing microorganisms, a secondborder zone and a second “death” zone. The positions and widths (shape)of the respective zones depend on the particular antibiotics, theconcentrations of the antibiotics (first and fourth concentrations andoptional second and third concentrations) and the particularmicroorganisms.

In another approach, step S2 comprises connecting the input of the firstfluid channel to the first fluid flow comprising a first test substanceat the first concentration and comprising a second test substance at athird concentration. Step S3 then comprises connecting the input of thesecond fluid channel to the second fluid flow lacking the first testsubstance or comprising the first test substance at the secondconcentration (that is lower than the first concentration) and lackingthe second test substance or comprising the second test substance at afourth concentration that is lower than the third concentration. A firstconcentration gradient of the first test substance and a secondconcentration gradient of the second test substance are thereby formedover at least a portion of the 3D culture matrix.

Step S4 comprises, in this embodiment, determining a response to themicroorganism to a mixture of the first and second test substances basedon a position of any border zone in the 3D culture matrix relative tothe first and/or second end portions or sides of the culture chamber.The border zone is between a first response zone in which themicroorganism shows a first response to the mixture and a secondresponse zone in which the microorganism shows a second, differentresponse to the mixture.

Hence, in this embodiment a concentration gradient of the first testsubstance is established from the first fluid channel (highconcentration of the first test substance) over at least a portion ofthe 3D culture matrix to the second fluid channel (low concentration ofthe first test substance). Correspondingly, a concentration gradient ofthe second test substance is established from the first fluid channel(high concentration of the second test substance) over at least aportion of the 3D culture matrix to the second fluid channel (lowconcentration of the second test substance).

This embodiment differs from the previous one in that the first fluidflow comprises the highest concentration of both test substances whereasin the previous embodiment the first fluid flow had the highestconcentration of the first test substance whereas the second fluid flowhad the highest concentration of the second test substance.

The present embodiment is thereby more appropriate for determining theresponse of microorganisms to a mixture or cocktail of test substances.The previous embodiment in clear contrast enables parallel testing oftwo test substances using a single fluidic device and a single culturechamber.

In an embodiment, the culture chamber of the fluidic device has at leastfour end portions or sides that can be connected to respective fluidflows. Hence, the culture chamber then additionally has a third fluidchannel flanking a third end portion or side of the culture chamber anda fourth channel flanking a fourth, different end portion or side of theculture chamber. In this embodiment, the test substance is a first testsubstance.

The method then comprises the additional steps of connecting an input ofthe third fluid channel to a third fluid flow comprising a second testsubstance at a third concentration and connecting an input of the fourthfluid channel to a fourth fluid flow lacking the second test substanceor comprising the second test substance at a fourth concentration thatis lower than the third concentration. Hence, a concentration gradientof the second test substance is formed over at least a portion of the 3Dculture matrix. In this embodiment, the method also comprisesdetermining a response of the microorganism to the second test substancebased on a position, relative to the third and/or fourth end portion orside, of any border zone in the 3D culture matrix. This border zone isbetween a first response zone in which the microorganism shows a firstresponse to the second test substance and a second response zone inwhich the microorganism shows a second, different response to the secondtest substance.

In this embodiment, two test substances can be tested in parallel. Forinstance, if the culture chamber and the 3D culture matrix has arectangular or quadratic cross-section then the concentration gradientof the first test substance can be established along the X directionbetween the first and second fluid channels, whereas the concentrationgradient of the second test substance is then established along the Ydirection between the third and fourth fluid channels.

Here below, a particular use of the method will be further describedwith the test substance being an antibiotic or other form of bactericideand/or bacteriostat. In this embodiment, step S4 of FIG. 1 comprisesdetermining susceptibility of the microorganism to the test substancebased on a position of the border zone in the 3D culture matrix relativeto the first and/or second end portion or side of the culture chamber.This border zone is then between a growth zone of growing microorganismand a non-growth zone lacking growth of the microorganism.

In this embodiment, an additional step as shown in FIG. 5 can beperformed. The method continues from step S4 of FIG. 1. The followingstep S40 determines resistance of the microorganism to the testsubstance based on a width of the border zone. Hence, if the border zonehas a non-zero width then microorganisms that are resistant to the testsubstance are able to grow in the concentration range corresponding tothe border zone. A variant of step S40 comprises determining resistanceof the microorganism to the test substance based on a shape of theborder zone.

FIG. 6 is a flow diagram illustrating an embodiment of step S4 of FIG. 1that can be used to determine MIC of the test substance from an imagetaken of the 3D culture matrix in step S21 of FIG. 3, for instance,using a bright-field or phase-contrast microscope. The method, thus,continues from step S22 in FIG. 3 and continues to step S50. This stepS50 comprises determining a relation of the detected light intensityversus position in the 3D culture matrix between the first end portionor side and the second, different end portion or side of the culturechamber. Hence, this step S50 basically corresponds to determining thedetected light intensity at different distances between the first endportion or side and the second end portion of the side. This relationcould, for instance, be in the form of a graph or plot showing how thedetected light intensity versus the distance between the first andsecond end portions of the culture chamber, see FIGS. 17B and 18B.

For instance, the 3D culture matrix could be regarded as a matrix ofrows and columns with detected light intensity values. In such a case, arow could represent the detected light intensity values when travellingfrom the first side of the 3D culture matrix towards the second,opposite side of the 3D culture matrix in the case of a rectangular orquadratic 3D culture matrix. Such a row is then parallel with thedirection of the concentration gradient. In an embodiment, an averagerow with average detected light intensity values is obtained bysummarizing the detected light intensity values of all rows and dividingthe respective summed values by the number of rows. Alternatively, a sumrow is calculated by summarizing the detected light intensity values ofall rows in a direction perpendicular to the direction of theconcentration gradient. The determination of the detected lightintensity at different distances can then be performed on the averagerow or the sum row.

A following step S51 then comprises determining a MIC of the testsubstance for the microorganism based on the relation.

FIG. 7 is a flow diagram illustrating in more detail how this MICdetermination can be performed. The method continues from step S50. Anext step S60 comprises identifying a position at which there is a kinkin a signal representing the relation between detected light intensityand position. This signal could thus be a representation of the graphsas shown in FIGS. 17B and 18B. Step S60, thus, investigates the signaland identifies the position at which there is a kink in the signal.

A next step S61 comprises converting the position identified in step S60and corresponding to the kink into a concentration of the test substancebased on predefined gradient information defining concentration versusposition in the 3D culture matrix. Hence, in this approach there is apredefined relation between the concentration of the test substance inthe 3D culture matrix and the position relative one of the end portions.

Generally, the concentration gradient is a linear concentration gradientat steady-state, i.e. ranging from the first concentration at the firstend portion or side to the second concentration or zero concentration atthe second end portion or side. In such a case, there is a simplerelation between the concentration of the test substance and thedistance or position relative to one of the end positions.

It is also possible to label, such as using a radioactive label, thetest substance or use an easily detectable, such as fluorescent,detection substance that has substantially similar diffusioncharacteristics, mainly dictated by the size of the molecule, throughthe 3D culture matrix as the test substance. In such a case, theconcentration gradient of the radioactively labelled test substance orthe detection substance could be easily measured and the predefinedgradient information defining concentration versus position in the 3Dculture matrix can be determined from such an experiment.

In either case, the predefined gradient information enables convertingthe position determined in step S60 into a concentration value thatcorresponds to the MIC of the test substance in step S61.

The time it takes to establish a steady-state gradient within the 3Dculture matrix depends on the width of the 3D culture matrix between thetwo fluid channels and the diffusions constant of the test substance.The diffusion constant is, in turn, dependent on the temperature, theviscosity of the 3D culture matrix and the radius of the molecules ofthe test substance. For example, ampicillin in agarose matrix has adiffusion constant of D=0.016 cm²/h [18].

FIGS. 9 to 15 illustrate portions of fluidic devices according todifferent embodiments showing various numbers and positions of fluidchannels and different configurations of culture chambers. The shownfigures should, however, merely be seen as a few illustrative examplesof the embodiments and further variants and modifications are possibleand within the scope of the embodiments.

FIG. 9 illustrates an embodiment of a fluidic device with a rectangularor quadratic culture chamber 10 having a first fluid channel 20 flankinga first side 12 and a second fluid channel 30 flanking a second,opposite side 14 of the culture chamber 10. In this embodiment, a linearconcentration gradient will be established during steady state over thewhole 3D culture matrix present in the culture chamber 10.

The two fluid channels do not necessarily have to flank opposite sidesof the culture chamber as shown in FIG. 9. FIG. 10 illustrates theculture chamber 10 with the first fluid channel 20 and the second fluidchannel flanking two adjacent sides 12, 16 of the culture chamber 10. Inthis embodiment, the concentration gradient will be established betweenthese two adjacent sides 12, 16.

It is, as has been discussed in the foregoing, possible to use more thantwo fluid channels. FIG. 11 illustrates an embodiment in which each side12, 14, 16, 18 of the culture chamber 10 is flanked by a respectivefluid channel 20, 30, 40, 50. In this approach two different testsubstances could be tested in order to establish a first linearconcentration gradient of a first test substance over the 3D culturematrix from the first fluid channel 20 to the second, opposite fluidchannel 30 (X direction). A second linear concentration gradient of asecond test substance over the 3D culture matrix can then be establishedfrom the third fluid channel 40 to the fourth, opposite fluid channel 50(Y direction).

In FIGS. 9-11 a rectangular or quadratic culture chamber 10 has beendisclosed. The embodiments are however not limited thereto. FIG. 12illustrates a culture chamber 10 having a triangular configuration witha first fluid channel 20 flanking a first side 12, a second fluidchannel 30 flanking a second, adjacent side 14 and optionally also athird fluid channel 40 flanking a third, adjacent side 16 of the culturechamber 10.

Also more complex culture chamber configurations with five, six, sevenor even more sides are possible. FIG. 13 illustrates a hexagonal culturechamber 10 having six sides 12, 14 and up to six fluid channels 20, 30,of which only two are marked with reference signs in the figure. Hence,in this embodiment it is possible to establish three different linearconcentration gradients and thereby testing three different testsubstances in a single fluidic device.

The fluidic device may also comprise circular or elliptical culturechambers 10 as schematically shown in FIG. 14. In such a case, the fluidchannels 20, 30 flank respective end portions 12, 14 of the culturechamber 10. These end portions 12, 14 correspond to different portionsof the circumference of the culture chamber 10 and thereby to differentportions of the lateral surface of the 3D culture matrix to be arrangedin the culture chamber 10.

In FIGS. 9-14 the fluid channels have been flanking end portions in theform of sides or portions of the circumference of the culture chamber.It is also, or alternatively, possible to have fluid channels 20, 30flanking end portions 12, 14 in terms of top or upper side or ceiling 12and bottom or lower side 14 of the culture chamber 10 as shown in FIG.15.

The present embodiments can be used to determine the identity of and tomonitor various microorganisms, test substances and responses. Hence,the embodiments find many different uses within hospital clinics,laboratories, diagnostic laboratories, healthcare facilities, etc.

For instance, the embodiments can be used to identify MIC, or otherconcentration thresholds that have an effect or no effect, of abioactive compound in order to identify the minimum concentration of thebioactive compound that has an effect on any given microorganism withregard to growth, proliferation, death or survival of the microorganism.

Furthermore, by establishing MIC for a set of different test substances,the phenotypic identity of a tested microorganism can be established in,for example, a diagnostic test. The analysis of phenotype could resultin either full identification of the microorganism strain or result in ageneral classification of the microorganism with regard to responses tovarious test substances.

The embodiments can also be used to follow the change of MIC for a testcompound on the growth, proliferation, viability or other behaviouralaspect of the microorganism over time. This approach enables monitoringof development or loss of resistance, such as antibiotic resistance, inthe microorganism over time through several generations, therebyaltering the ability of the microorganism to metabolize or resist theeffects of the test substance. This type of experiment can be used toprovide an indication of suitable clinical dose of the test substanceand/or frequency of administration. Hence, the embodiments can be usedto study both the pharmacodynamics and the pharmacokinetics of any testsubstance or combination of test substances in any given type ofmicroorganism.

The embodiments can further be used to evaluate and identifycombinations of test substances, such as antibiotics, which together aremore efficient than the individual substances, or to evaluate if thetest substances have synergistic effect, or if they together have noeffects on, for example, the growth, proliferation, viability or otherbehavioural aspect of the microorganism.

The embodiments can be used to screen novel drugs or chemical compoundsfor their effects on microorganism growth, proliferation, viability,death, ability to spread, or other behavioural aspects of themicroorganism.

The embodiments can also be used to quickly get a first profile ofresponse of any given microorganism to substances used in clinicalpractice. The aim could then be to identify substances that are suitablefor anti-microorganism treatment of patients suffering from microbialinfections. This can be used even in cases where the life of the patientdepends on a fast identification of the microorganism causing theinfection in order to design an appropriate treatment.

The embodiments can further be used to study the effects of drugs ortest substances on host cells that have been infected with viruses, witheffects on cell behaviour, cell survival, cell proliferation, cell deathand/or cell differentiation used as readouts for the amount and effectof the viruses and test substances on the host cells. In thisapplication, the viruses are preferably placed together with the cellsthat they are known to be able to infect. Thus, both direct effects onthe virus particles as well as on the infected host cells, such ascytopathic effects, can be used to study the effects of test substancesat different concentrations.

As an example of the study of the effects of drugs on parasites, Malariaparasites could be studied using human or mouse red blood cells infectedwith the parasite and cultured in the 3D culture matrix of the fluidicdevice. The response of the parasites and red blood cells to one or moregradients of drug(s) can then be tested.

Culturing microorganisms in a 3D culture matrix in a culture chamber ofa fluidic device enables keeping the microorganisms inside an at leastpartly closed culture chamber. This provides protection for thepersonnel against potentially harmful microorganisms but also protectsagainst contamination of the test sample in the 3D culture matrix.

Another aspect of the embodiments relates, see FIG. 16, to a system 60for determining a response of a microorganism to a test substance. Thesystem 60 comprises a fluidic device represented by the culture chamber10 and flanking channels in the figure. The fluidic device comprises aculture chamber 10 configured to house a culture of the microorganism ina 3D culture matrix. The fluidic device also comprises a first fluidchannel flanking a first end portion or side of the culture chamber 10and a second fluid channel flanking a second, different end portion orside of the culture chamber 10. The system 60 further comprises a firstfluid reservoir (see FIG. 8) comprising a first fluid comprising thetest substance at a first concentration. The first fluid reservoir isconfigured to be connected to an input of the first fluid channel. Thesystem 60 also comprises a second fluid reservoir comprising a secondfluid lacking the test substance or comprising the test substance at asecond concentration that is lower than the first concentration. Thesecond fluid reservoir is configured to be connected to an input of thesecond fluid channel to form a concentration gradient of the testsubstance over at least a portion of the 3D culture matrix.

The system 60 also comprises a computer-based system 62, 66 configuredto take at least one image of the 3D culture matrix and process the atleast one image to identify a position, relative to the first endportion and/or second, different end portion, of any border zone in the3D culture matrix. This border zone is between a first response zone inwhich the microorganism shows a first response to the test substance anda second response zone in which the microorganism shows a second,different response to the test substance. The computer-based system 62,66 is also configured to determine a response of the microorganism tothe test substance based on the position of the border zone.

In FIG. 16 the computer-based system 62, 66 has been exemplified by acamera or other image or signal capturing equipment or detector 66. Thiscamera or detector 66 is preferably, but not necessarily, connected toor arranged in relation to a microscope 68 as shown in the figure inorder to take the picture of the 3D culture matrix. The camera 66 ispreferably connected to a computer 62 comprising a memory configured tostore the image data and a computer program comprising code means to beexecuted by a processing unit of the computer 62. The computer programis then configured to identify the position and optionally the widthand/or shape of the border zone in the image, such as based on detectedlight intensity or detected fluorescence. The computer program ispreferably also configured to convert the position of the border zoneinto a concentration value or a range of concentration values for thetest substance as previously disclosed herein.

An optional screen 64 of the system 60 can be connected to the computer62 in order to display the captured image (FIG. 17A or 18A), a processedgraph showing detected light intensity or detected fluorescence versusposition in the 3D culture matrix or versus concentration of the testsubstance along the concentration gradient (FIG. 17B or 18B), and/or thedetermine concentration or concentration range.

Another aspect of the embodiments relates to use of a fluidic device todetermine a response of a microorganism to a test substance. The fluidicdevice comprises a culture chamber configured to a house a culture ofthe microorganism in a 3D culture matrix. The fluidic device alsocomprises a first fluid channel flanking a first end portion of theculture chamber and configured to carry a first fluid flow comprisingthe test substance at a first concentration. The fluidic device furthercomprises a second fluid channel flanking a second, different endportion of the culture chamber and configured to carry a second fluidlacking the test substance or comprising the test substance at a secondconcentration that is lower than the first concentration to form aconcentration gradient of the test substance over at least a portion ofthe 3D culture matrix. The use comprises determining the response of themicroorganism to the test substance based on a position of any borderzone in the 3D culture matrix relative to the first end portion and/orthe second, different end portion. The border zone is between a firstresponse zone in which the microorganism shows a first response to thetest substance and a second response zone in which the microorganismshows a second, different response to the test substance.

EXPERIMENTS Experiment 1—Ampicillin

Bacterium strain E. coli K12 MG1655 was cultured on a Luria broth (LB)plate. The E. coli cells were diluted by phosphate buffered saline (PBS)to OD₆₀₀=0.1 as measured by a MULTISKAN® FC Microplate Photometer(Thermo Scientific). Same volumes of PBS with OD₆₀₀=0.1 cells andlow-melting temperature agarose were mixed together. A pipette withwhite tips was used to suck up 8 μl of the mixture and inject themixture into the culture chamber of a microfluidic device CELLDIRECTOR®Ruby (Gradientech AB), see upper panel in FIG. 20. The fluid channelinputs of the microfluidic device were connected to fluid reservoirscomprising Muelle-Hinton medium and where one of the reservoirs alsocontained 20 μg/ml ampicillin. The speed of a pusher used to draw themedium into the fluid channels was set to 5 μl/min for 30 minutes andthen to 2 μl/min for the rest of the time.

The microfluidic device was put on an Eclipse TE2000 Nikon invertedmicroscope system connected to a charged coupled device (CCD) camera.The microfluidic device was connected to a thermal stat to maintain thetemperature in the 3D culture matrix at 37° C. during the experiment. Inthe present experiments the 2× objective lens was used so that the wholeculture chamber was in the field of vision of the microscope. Followingbrightness and focal distance adjustment time-lapse photography of a CCDcamera supported software (1 picture/30 s) was turned on.

The pictures were cut to match a selected central portion of the culturechamber, see black box in FIGS. 17A and 18A. Image processing softwarewas used to extract detected light intensity data from the pictures. Aspatial growth situation distribution diagram was used to summarize thegrey-scale values, i.e. detected light intensity values, of all thelines that are perpendicular to the direction of the gradient as theY-axis with the concentration gradient as the X-axis.

A significant point, representing MIC of the ampicillin, can be found inthis chart. A diagram of the cell growth rate, represented by opticalintensity, was also drawn as shown in FIG. 17B.

FIG. 17A illustrates the significant cell growth close to the sink fluidchannel where concentration of ampicillin is low. The E. coli cellscorrespond to the white band seen in the figure. FIG. 17B illustratesthe cell growth versus the concentration gradient of the ampicillin. TheMIC was determined to be 5 μg/ml in this experiment. FIG. 17Cillustrates the concentration gradient of ampicillin formed in the 3Dculture matrix.

Please note that the top seen around 10 μg/ml in FIG. 17B is due to atear in the 3D culture matrix.

Experiment 2—Spectinomycin

This experiment was performed as in Experiment 1 with the exception that50 μg/ml spectinomycin was added to one of the fluid reservoirs insteadof ampicillin. The results are shown in FIGS. 18A-180.

FIGS. 18A and 18B clearly demonstrate a much wider border as compared toExperiment 1 (FIGS. 17A and 17B). Hence, this experiment indicated thepresence of spectinomycin resistance among the E. coli cells, whereas nocorresponding ampicillin resistance was detected in Experiment 1.

FIG. 19 illustrates the average grey scale value, i.e. detectedintensity and thereby cell density, at different positions in the 3Dculture matrix over time. These different positions correspond toconcentrations of 0, 12.5, 25, 37.5 and 50 μg/ml spectinomycin.

The embodiments described above are to be understood as a fewillustrative examples of the present invention. It will be understood bythose skilled in the art that various modifications, combinations andchanges may be made to the embodiments without departing from the scopeof the present invention. In particular, different part solutions in thedifferent embodiments can be combined in other configurations, wheretechnically possible. The scope of the present invention is, however,defined by the appended claims.

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1. A system for determining a response of a microorganism to a testsubstance, the system comprising: a fluidic device comprising: a culturechamber configured to house a culture of the microorganism in a threedimensional (3D) culture matrix; a first fluid channel flanking a firstend portion of the culture chamber; and a second fluid channel flankinga second, different end portion of the culture chamber; a first fluidreservoir comprising a first fluid comprising the test substance at afirst concentration, the first fluid reservoir is configured to beconnected to an input of the first fluid channel; a second fluidreservoir comprising a second fluid lacking the test substance orcomprising the test substance at a second concentration that is lowerthan the first concentration, the second fluid reservoir is configuredto be connected to an input of the second fluid channel to form aconcentration gradient of the test substance over at least a portion ofthe 3D culture matrix; and a computer-based system configured to i) takeat least one image of the 3D culture matrix, ii) process the at leastone image to identify a position, relative to the first end portionand/or the second, different end portion, of any border zone in the 3Dculture matrix between a growth zone of growing microorganism and anon-growth zone lacking growth of the microorganism, wherein the growthof the microorganism in the growth zone is not inhibited by the testsubstance, iii) process the at least one image to identify a width ofthe any border zone, iv) determine a minimal inhibitory concentration(MIC) of the microorganism to the test substance based on the positionof the any border zone by correlating the position to a concentration ora concentration range of the test substance based on gradientinformation defining concentration versus position in the 3D culturematrix for the concentration gradient, and v) determine a resistance ofthe microorganism to the test substance based on the width of the anyborder zone.
 2. The system according to claim 1, further comprising atleast one pump configured to pump the first fluid from the first fluidreservoir into the input of the first fluid channel and out through anoutput of the first fluid channel and pump the second fluid from thesecond fluid reservoir into the input of the second fluid channel andout through an output of the second fluid channel.
 3. The systemaccording to claim 1, wherein the computer-based system is configured totake the at least one image of the 3D culture matrix at least afterformation of a steady-state concentration gradient of the test substanceover the at least a portion of the 3D culture matrix.
 4. The systemaccording to claim 1, wherein the test substance is a first testsubstance and the concentration gradient is a first concentrationgradient; the first fluid reservoir comprises the first fluid i)comprising the first test substance at the first concentration, and ii)lacking a second test substance or comprising the second test substanceat a third concentration; the second fluid reservoir comprises thesecond fluid i) lacking the first test substance or comprising the firsttest substance at the second concentration, and ii) comprising thesecond test substance at a fourth concentration that is higher than thethird concentration to form the first concentration gradient of thefirst test substance and a second concentration gradient of the secondtest substance over the at least a portion of the 3D culture matrix; thecomputer-based system is configured to ii) process the at least oneimage to identify respective positions, relative to the first endportion and/or the second, different end portion, of any one or moreborder zones in the 3D culture matrix between a growth zone of growingmicroorganism and a respective non-growth zone lacking growth of themicroorganism, wherein the growth of the microorganism in the growthzone is not inhibited by the first test substance or the second testsubstance, iii) process the at least one image to identify respectivewidths of the any one or more border zones, iv) determine a MIC of themicroorganism to the first test substance and the second test substancebased on the respective positions of the any one or more border zones bycorrelating the respective positions to a concentration or aconcentration range of the respective test substance based on gradientinformation defining concentration versus position in the 3D culturematrix for the respective concentration gradient, and v) determine theresistance of the microorganism to the first test substance and thesecond test substance based on the respective widths of the any one ormore border zones.
 5. The system according to claim 1, wherein the testsubstance is a first test substance and the concentration gradient is afirst concentration gradient; the first fluid reservoir comprises thefirst fluid i) comprising the first test substance at the firstconcentration, and ii) comprising a second test substance at a thirdconcentration; the second fluid reservoir comprises the second fluid i)lacking the first test substance or comprising the first test substanceat the second concentration, and ii) lacking the second test substanceor comprising the second test substance at a fourth concentration thatis lower than the third concentration to form the first concentrationgradient of the first test substance and a second concentration gradientof the second test substance over the at least a portion of the 3Dculture matrix; the computer-based system is configured to ii) processthe at least one image to identify respective positions, relative to thefirst end portion and/or the second, different end portion, of any oneor more border zones in the 3D culture matrix between a growth zone ofgrowing microorganism and a respective non-growth zone lacking growth ofthe microorganism, wherein growth of the microorganism in the growthzone is not inhibited by the first test substance or the second testsubstance, iii) process the at least one image to identify respectivewidths of the any one or more border zones, iv) determine a MIC of themicroorganism to the first test substance and the second test substancebased on the respective positions of the any one or more border zones bycorrelating the respective position to a concentration or aconcentration range of the respective test substance based on gradientinformation defining concentration versus position in the 3D culturematrix for the respective concentration gradient, and v) determine theresistance of the microorganism to the first test substance and thesecond test substance based on the respective widths of the any one ormore border zones.
 6. The system according to claim 1, wherein the testsubstance is a first test substance, the concentration gradient is afirst concentration gradient, the growth zone is a first growth zone andthe non-growth zone is a first non-growth zone; the fluidic devicecomprises: a third fluid channel flanking a third end portion of theculture chamber; and a fourth fluid channel flanking a fourth, differentend portion of the culture chamber; a third fluid reservoir comprising athird fluid comprising a second test substance at a third concentration,the third fluid reservoir is configured to be connected to an input ofthe third fluid channel; a fourth fluid reservoir comprising a fourthfluid lacking the second test substance or comprising the second testsubstance at a fourth concentration that is lower than the firstconcentration, the fourth fluid reservoir is configured to be connectedto an input of the fourth fluid channel to form a second concentrationgradient of the second test substance over at least a portion of the 3Dculture matrix; and the computer-based system configured to ii) processthe at least one image to identify a second position, relative to thirdfirst end portion and/or the fourth, different end portion, of anyadditional border zone in the 3D culture matrix between a second growthzone of growing microorganism and a second non-growth zone lackinggrowth of the microorganism, wherein growth of the microorganism in thesecond growth zone is not inhibited by the second test substance, iii)process the at least one image to identify a second width of the anyadditional border zone, iv) determine a MIC of the microorganism to thesecond test substance based on the second position of the any additionalborder zone by correlating the second position to a concentration or aconcentration range of the second test substance based on gradientinformation defining concentration versus position in the 3D culturematrix for the second concentration gradient, and v) determine aresistance of the microorganism to the second test substance based onthe second width of the any additional border zone.
 7. The systemaccording to claim 1, wherein the computer-based system is configured todetect light intensity in the at least one image, and identify the anyborder zone in the 3D culture matrix based on the detected lightintensity.